Surveillance of fish species composition using environmental DNA

Prompt and accurate methods for assessing the species composition of given areas are indispensable in addressing the rapid loss of biodiversity. Here, we propose a method for the surveillance of fish species composition in freshwater using environmental DNA as species markers. First, the applicability of the method was demonstrated through aquarium experiments. DNA was extracted from 120 ml aquarium water, and the degenerated primers targeting the fish mitochondrial cytochrome b gene were used for amplification. PCR-amplified fragments were analysed by random cloning, and all species reared in the aquarium were detected. Next, this method was applied to natural freshwater environments. Water samples were collected from three sites in the Yura River, Japan; DNA was concentrated from 2 l of environmental water, and then amplified and cloned. Up to four species of fish were detected by sequencing 47 randomly selected clones from a single water sample. Overall, the results were consistent with previous knowledge of fish habitat utilisation. Using this method, the surveillance of fish species composition can be conducted less laboriously than with traditional methods.